Journal: bioRxiv

Article Title: EpiPred: A gene-specific machine learning model for classifying missense variants in the epilepsy-related gene STXBP1

doi: 10.1101/2025.08.09.669488

Figure Lengend Snippet: ( A ) Overview of the approach adopted for the generation of the EpiPred model, including the input datasets (blue) and the functional testing of the EpiPred predictions using three biochemical assays (stability, abundance, solubility) and STX1 interaction in an overexpression model system (yellow). ( B ) Comparison of area under the receiver operator curve (AUROC) for EpiPred and a subset of high-performing globally-trained VEPs across the full truth set. ( C ) EpiPred Probability of PLP (EpiPred-P PLP ) score distributions in the full truth set separated by class as well as the full set of VUS. EpiPred-P PLP scores of 1 suggest pathogenicity, while scores of 0 suggest neutrality ( D ) EpiPred-P PLP output for known PLP and BLB variants used in the truth set mapped onto hSTXBP1 predicted structure (AlphaFold structure: AF-P61764-F1-model_v4), EpiPred-P PLP scores close to 1 are shown in purple, while scores close to zero appear in green.

Article Snippet: Following SDS-PAGE and transfer to PVDF membrane, samples were probed with anti-STX1 antibody (1:1000, 18572, Cell Signaling Technology).

Techniques: Functional Assay, Solubility, Over Expression, Comparison

Journal: bioRxiv

Article Title: EpiPred: A gene-specific machine learning model for classifying missense variants in the epilepsy-related gene STXBP1

doi: 10.1101/2025.08.09.669488

Figure Lengend Snippet: Data from representative western blots (left) and quantification (right) are plotted for the WT STXBP1 and twenty missense variants. Each assay is plotted separately: (A) Abundance, ( B ) Stability, ( C ) Solubility, and ( D ) STX1 PPI. Scores are normalized to the WT reference allele score. The quantified data is sorted, left to right, by EpiPred-P PLP score from lowest (likely benign) to highest (likely pathogenic) and colored by class (wildtype, PLP, BLB, VUS predicted PLP/BLB). n=3, * p-value < 0.05, all raw data and p-values in Table S5,6 .

Article Snippet: Following SDS-PAGE and transfer to PVDF membrane, samples were probed with anti-STX1 antibody (1:1000, 18572, Cell Signaling Technology).

Techniques: Western Blot, Solubility

Journal: International Journal of Molecular Sciences

Article Title: The E3 Ubiquitin Ligase PRAJA1: A Key Regulator of Synaptic Dynamics and Memory Processes with Implications for Alzheimer’s Disease

doi: 10.3390/ijms26072909

Figure Lengend Snippet: Figure 2. Pja1 Knockdown in CA1 Reduces Spine Density and Alters Synaptic Protein Expression. (A) Schematic of bilateral lentiviral injection targeting the CA1 region. (B) Representative immunoflu- orescence images of the CA1 region showing GFP expression (green), DAPI nuclear staining (blue), and merged images of mice injected with either scrambled shRNA (sc shRNA, top row) or Pja1 shRNA (bottom row) are shown. Scale bar: 100 µm. (C) Quantification of PRAJA1 protein levels following lentiviral injection, showing a significant reduction in the Pja1 shRNA group. (n = 8 sc shRNA, n = 7 Pja1 shRNA, unpaired t-test, *** p = 0.0005). (D) Representative images of dendritic spines (top) and quantification of spine density (bottom), demonstrating a significant decrease in Pja1 knockdown mice. Scale bar: 5 µm. (n = 33 spines from 3 mice per group; unpaired t-test; **** p < 0.0001). (E) Representative Western blots and quantification of pre-synaptic protein levels, showing significant reductions in Munc18-1 and SNAP-25 in the Pja1 shRNA group. (Munc18-1: n = 7 per group, * p = 0.025; SNAP-25: sc shRNA: n = 7; Pja1 shRNA: n = 9, p > 0.05, ** p = 0.006; syntaxin 1A: sc shRNA: n = 8; Pja1 shRNA: n = 7, p > 0.05 ns, unpaired t-test). (F) Representative Western blots and quantification of post-synaptic protein levels, revealing a significant reduction in PSD-95 in the Pja1 shRNA group (Synapsin (total and phosphorylated): sc shRNA: n = 8; Pja1 shRNA: n = 7, p > 0.05 ns; PSD-95: sc shRNA: n = 10; Pja1 shRNA: n = 11, p > 0.05, ** p = 0.008 unpaired t-test.

Article Snippet: The following antibodies were used: PRAJA1 (1:1000, ProteinTech, Chicago, IL, USA, 17687-1-AP), actin (1:1000, Cell Signaling, Danvers, MA, USA, CST:4970s), Cav1.2 (1:500, Alomone, Jerusalem, Israel, ACC-003), Cav1.3 (1:500, Alomone, Jerusalem, Israel, ACC-005), SNAP25 (1:1000, CST:5309s), Munc18-1 (1:1000, CST:d406v), rabbit anti-PSD-95 (1:1000, CST:2507s), spinophilin (1:1000, CST:14136s), and synapsin (1:1000, CST:2312s). p-synapsin (1:1000, Cell Signaling, Danvers, MA, USA, CST:2311s), syntaxin 1A (1:1000, CST: 13002s).

Techniques: Knockdown, Expressing, Injection, Staining, shRNA, Western Blot